Hm, did you look at CCleaner at all, Rob?
I had the annoying invisible systray icon problem where during the occasional reboot, random systray icons would be simply "blank" and the associated icon/program functionality wouldn't work even though the tooltips described what the icon was supposed to be. I had to resort to using CCleaner's "tray notification icon" option. It deleted a few hundred MB's of icon & program cache in the AppData folder, and after I terminated and restarted Explorer it rebuilt the cache and fixed the problem completely.
Not exactly your problem I know, but I'd half wonder if some of the other myriad of options the program offers might've worked for ya.
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